Antibiotic activity altered by competitive interactions between two coral reef – associated bacteria

Microbes produce natural products that mediate interactions with each other and with their environments, representing a potential source of antibiotics for human use. The biosynthesis of some antibiotics whose constitutive production otherwise remains low has been shown to be induced by competing microbes. Competition among macroorganism hosts may further influence the metabolic outputs of members of their microbiomes, especially near host surfaces where hosts and microbial symbionts come into close contact. At multiple field sites in Fiji, we collected matched samples of corals and algae that were freestanding or in physical contact with each other, cultivated bacteria from their surfaces, and explored growth-inhibitory activities of these bacteria against marine and human pathogens. In the course of the investigation, an interaction was discovered between two coral-associated actinomycetes in which an Agrococcus sp. interfered with the antibiotic output of a Streptomyces sp. Several diketopiperazines identified from the antibiotic-producing bacterium could not, on their own, account for the antibiotic activity indicating that other, as yet unidentified molecule(s) or molecular blends, possibly including diketopiperazines, are likely involved. This observation highlights the complex molecular dynamics at play among microbiome constituents. The mechanisms through which microbial interactions impact the biological activities of specialized metabolites deserve further attention considering the ecological and commercial importance of bacterial natural products

The influence of deoxygenation on Caribbean coral larval settlement and early survival

Deoxygenation is emerging as a major threat to coral reefs where it can have catastrophic effects, including mass coral mortality. Some coral species cannot survive more than a few days of exposure to low oxygen conditions, while others can tolerate deoxygenation for weeks, suggesting that coral tolerance to lowered dissolved oxygen (DO) concentrations is species-specific. However, hypoxia thresholds for corals have not yet been fully defined, and more information is needed to understand if tolerance to deoxygenation is consistent across all life stages. In this study, we tested the influence of severe (1.5 mg L-1 DO) and intermediate (3.5 mg L-1 DO) deoxygenation on larval settlement and survival during the early recruitment life phase of Colpophyllia natans, Orbicella faveolata, and Pseudodiploria strigosa. Exposure to deoxygenation over a 3-day settlement period did not significantly impact larval survival nor settlement rates compared to ambient DO concentrations (6 mg L-1 DO) for all three species. However, recruit survivorship in C. natans and O. faveolata after further exposure to severe deoxygenation was reduced compared to intermediate deoxygenation and control DO conditions. After 45 days of exposure to severe deoxygenation only 2.5 ± 2.5% of the initial O. faveolata had survived the larval and recruit stages compared to 22.5 ± 4.5% in control oxygen conditions. Similarly, C. natans survival was 13.5 ± 6.0% under severe deoxygenation, compared to 41.0 ± 4.4% in the control treatment. In contrast, survival of P. strigosa larvae and recruits was not different under deoxygenation treatments compared to the control, and higher overall, relative to the other species, indicating that P. strigosa is more resilient to severe deoxygenation conditions during its earliest life stages. This study provides unique insights into species-specific variation in the tolerance of coral recruits to deoxygenation with implications for whether this life history stage may be a demographic bottleneck for three ecologically important Caribbean coral species. Given the increasing frequency and severity of deoxygenation events in Caribbean coastal waters, these results are an important contribution to the growing body of research on deoxygenation as a threat to coral reef persistence in the Anthropocene, with implications for conservation and restoration efforts integrating coral recruitment into reef recovery efforts

A community resource for paired genomic and metabolomic data mining

Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.Peer reviewe

Chemical ecology of marine microbial communities: An assessment of bacterial diversity and dynamics in tropical marine sediments

Marine sediments cover ~70% of the earth and host rich and diverse microbial communities. These microbial communities play an integral role in global nutrient cycling and the food web. They can be both a source of disease and/or an agent of mitigation through the natural products they produce, which can have cascading impacts on community structure and ecosystem function. Despite their importance, marine sediment microbes remain woefully understudied. The goal of this dissertation was to use next generation sequencing technology and newly developed bioinformatic pipelines to gain insight into these complex communities. First, I sought to reevaluate the 1% culturability paradigm by comparing sediment microbial communities using culture-dependent and culture-independent techniques. This comparative approach not only highlighted that >1% of sediment bacteria could be cultured, but also revealed the biases associated with culture-independent methods. Thirty-nine genera were identified in culture that were not detected with culture-independent methods, including some taxa that were fairly divergent from known cultured representatives. Next, I wanted to assess connections between sediment microbial communities, the sediment metabolome and sediment characteristics across varying spatial scales. To do this, microbial communities were sampled at three spatial scales, 1 m2 quadrats, 10 m transects, and sites across a 12 km2 area. Additionally, a small molecule in situ resin capture (SMIRC) method was employed to capture the metabolome present in sediments. The results from this study indicate that microbial diversity significantly increases with spatial scale and that sediment characteristics, such as grain size and nitrate concentrations, are significantly correlated with microbial communities. The SMIRC method was able to capture natural products and revealed the vast chemical landscape of marine sediments, much of which remains unexplored. Finally, I sought to evaluate how microbial communities in marine sediments vary in relation to the surrounding benthic environment by comparing fringing and back reefs of Mo’orea, French Polynesia. Even within a small area, ~1 km2, fringing and back reef sediment communities were distinct from each other. Back reefs exhibited greater richness and diversity in the microbial communities while fringing reefs had greater metabolomic richness. Supervised correlative analyses identified connections between microbes, metabolites and environmental characteristics such as nutrient concentration. Many of the taxa identified in the network analyses belong to relatively unknown lineages, providing important insight into the role these lineages may be playing in their communities. In conclusion, the results of this dissertation provide fundamental baseline information about the microbial communities and metabolites associated with marine sediments

Detection of Natural Products and Their Producers in Ocean Sediments.

Thousands of natural products have been identified from cultured microorganisms, yet evidence of their production in the environment has proven elusive. Technological advances in mass spectrometry, combined with public databases, now make it possible to address this disparity by detecting compounds directly from environmental samples. Here, we used adsorbent resins, tandem mass spectrometry, and next-generation sequencing to assess the metabolome of marine sediments and its relationship to bacterial community structure. We identified natural products previously reported from cultured bacteria, providing evidence they are produced in situ, and compounds of anthropogenic origin, suggesting this approach can be used as an indicator of environmental impact. The bacterial metabolite staurosporine was quantified and shown to reach physiologically relevant concentrations, indicating that it may influence sediment community structure. Staurosporine concentrations were correlated with the relative abundance of the staurosporine-producing bacterial genus Salinispora and production confirmed in strains cultured from the same location, providing a link between compound and candidate producer. Metagenomic analyses revealed numerous biosynthetic gene clusters related to indolocarbazole biosynthesis, providing evidence for noncanonical sources of staurosporine and a path forward to assess the relationships between natural products and the organisms that produce them. Untargeted environmental metabolomics circumvents the need for laboratory cultivation and represents a promising approach to understanding the functional roles of natural products in shaping microbial community structure in marine sediments.IMPORTANCE Natural products are readily isolated from cultured bacteria and exploited for useful purposes, including drug discovery. However, these compounds are rarely detected in the environments from which the bacteria are obtained, thus limiting our understanding of their ecological significance. Here, we used environmental metabolomics to directly assess chemical diversity in marine sediments. We identified numerous metabolites and, in one case, isolated strains of bacteria capable of producing one of the compounds detected. Coupling environmental metabolomics with community and metagenomic analyses provides opportunities to link compounds and producers and begin to assess the complex interactions mediated by specialized metabolites in marine sediments

Detection of Natural Products and Their Producers in Ocean Sediments.

Thousands of natural products have been identified from cultured microorganisms, yet evidence of their production in the environment has proven elusive. Technological advances in mass spectrometry, combined with public databases, now make it possible to address this disparity by detecting compounds directly from environmental samples. Here, we used adsorbent resins, tandem mass spectrometry, and next-generation sequencing to assess the metabolome of marine sediments and its relationship to bacterial community structure. We identified natural products previously reported from cultured bacteria, providing evidence they are produced in situ, and compounds of anthropogenic origin, suggesting this approach can be used as an indicator of environmental impact. The bacterial metabolite staurosporine was quantified and shown to reach physiologically relevant concentrations, indicating that it may influence sediment community structure. Staurosporine concentrations were correlated with the relative abundance of the staurosporine-producing bacterial genus Salinispora and production confirmed in strains cultured from the same location, providing a link between compound and candidate producer. Metagenomic analyses revealed numerous biosynthetic gene clusters related to indolocarbazole biosynthesis, providing evidence for noncanonical sources of staurosporine and a path forward to assess the relationships between natural products and the organisms that produce them. Untargeted environmental metabolomics circumvents the need for laboratory cultivation and represents a promising approach to understanding the functional roles of natural products in shaping microbial community structure in marine sediments.IMPORTANCE Natural products are readily isolated from cultured bacteria and exploited for useful purposes, including drug discovery. However, these compounds are rarely detected in the environments from which the bacteria are obtained, thus limiting our understanding of their ecological significance. Here, we used environmental metabolomics to directly assess chemical diversity in marine sediments. We identified numerous metabolites and, in one case, isolated strains of bacteria capable of producing one of the compounds detected. Coupling environmental metabolomics with community and metagenomic analyses provides opportunities to link compounds and producers and begin to assess the complex interactions mediated by specialized metabolites in marine sediments

The Natural Product Domain Seeker version 2 (NaPDoS2) webtool relates ketosynthase phylogeny to biosynthetic function.

The Natural Product Domain Seeker (NaPDoS) webtool detects and classifies ketosynthase (KS) and condensation domains from genomic, metagenomic, and amplicon sequence data. Unlike other tools, a phylogeny-based classification scheme is used to make broader predictions about the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes in which these domains are found. NaPDoS is particularly useful for the analysis of incomplete biosynthetic genes or gene clusters, as are often observed in poorly assembled genomes and metagenomes, or when loci are not clustered, as in eukaryotic genomes. To help support the growing interest in sequence-based analyses of natural product biosynthetic diversity, here we introduce version 2 of the webtool, NaPDoS2, available at http://napdos.ucsd.edu/napdos2. This update includes the addition of 1417 KS sequences, representing a major expansion of the taxonomic and functional diversity represented in the webtool database. The phylogeny-based KS classification scheme now recognizes 41 class and subclass assignments, including new type II PKS subclasses. Workflow modifications accelerate run times, allowing larger datasets to be analyzed. In addition, default parameters were established using statistical validation tests to maximize KS detection and classification accuracy while minimizing false positives. We further demonstrate the applications of NaPDoS2 to assess PKS biosynthetic potential using genomic, metagenomic, and PCR amplicon datasets. These examples illustrate how NaPDoS2 can be used to predict biosynthetic potential and detect genes involved in the biosynthesis of specific structure classes or new biosynthetic mechanisms

DataSheet_1_The influence of deoxygenation on Caribbean coral larval settlement and early survival.csv

Deoxygenation is emerging as a major threat to coral reefs where it can have catastrophic effects, including mass coral mortality. Some coral species cannot survive more than a few days of exposure to low oxygen conditions, while others can tolerate deoxygenation for weeks, suggesting that coral tolerance to lowered dissolved oxygen (DO) concentrations is species-specific. However, hypoxia thresholds for corals have not yet been fully defined, and more information is needed to understand if tolerance to deoxygenation is consistent across all life stages. In this study, we tested the influence of severe (1.5 mg L-1 DO) and intermediate (3.5 mg L-1 DO) deoxygenation on larval settlement and survival during the early recruitment life phase of Colpophyllia natans, Orbicella faveolata, and Pseudodiploria strigosa. Exposure to deoxygenation over a 3-day settlement period did not significantly impact larval survival nor settlement rates compared to ambient DO concentrations (6 mg L-1 DO) for all three species. However, recruit survivorship in C. natans and O. faveolata after further exposure to severe deoxygenation was reduced compared to intermediate deoxygenation and control DO conditions. After 45 days of exposure to severe deoxygenation only 2.5 ± 2.5% of the initial O. faveolata had survived the larval and recruit stages compared to 22.5 ± 4.5% in control oxygen conditions. Similarly, C. natans survival was 13.5 ± 6.0% under severe deoxygenation, compared to 41.0 ± 4.4% in the control treatment. In contrast, survival of P. strigosa larvae and recruits was not different under deoxygenation treatments compared to the control, and higher overall, relative to the other species, indicating that P. strigosa is more resilient to severe deoxygenation conditions during its earliest life stages. This study provides unique insights into species-specific variation in the tolerance of coral recruits to deoxygenation with implications for whether this life history stage may be a demographic bottleneck for three ecologically important Caribbean coral species. Given the increasing frequency and severity of deoxygenation events in Caribbean coastal waters, these results are an important contribution to the growing body of research on deoxygenation as a threat to coral reef persistence in the Anthropocene, with implications for conservation and restoration efforts integrating coral recruitment into reef recovery efforts.</p

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages

n our daily lives, we consume foods that have been transported, stored, prepared, cooked, or otherwise processed by ourselves or others. Food storage and preparation have drastic effects on the chemical composition of foods. Untargeted mass spectrometry analysis of food samples has the potential to increase our chemical understanding of these processes by detecting a broad spectrum of chemicals. We performed a time-based analysis of the chemical changes in foods during common preparations, such as fermentation, brewing, and ripening, using untargeted mass spectrometry and molecular networking. The data analysis workflow presented implements an approach to study changes in food chemistry that can reveal global alterations in chemical profiles, identify changes in abundance, as well as identify specific chemicals and their transformation products. The data generated in this study are publicly available, enabling the replication and re-analysis of these data in isolation, and serve as a baseline dataset for future investigations